When I assembly sequences using cap3 the sequences the assembly viewer does not reverse complement sequences correctly.

I am using UGENE 1.9.5 on windows xp and OsX with similar results


I have created a sequence and assembling it with its reverse complement  does not give the correct alignment. I have attached a fasta files and screen shot to demonstrate.

Is this a bug or am I not carrying out the assembly correctly?

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Hi Rob,

I've investigated the issue - it's a bug of CAP3 program. Problem is related to incorrect ACE file generation. Unfortunately we don't have access to CAP3 source code, but I will try to contact the author to report about this problem.

Meanwhile we will prepare a workaround for this issue, based on analysis of "native" output of CAP3. I will update this thread when the fix is ready.

Please note, although the reverse complement reads are not included into the resulting alignment, the contig sequence is correct.

On MacOS the behavior is different and related to viewer. And on Windows the CAP3  executable is replaced with newer one.

In result the issue is fully fixed, the bugfix is included into 1.9.6 which is released this week.

Hi Konstantin,

I will upgrade to 1.9.6.

Thanks for looking into the problem and thanks for providing a great tool for us all.

Oh, sure, no better  source to learn than a bug report.

BTW, there should be a way (button?) to easily report spammers or at least a given message as spam...

Quote:

Oh, sure, no better  source to learn than a bug report. BTW, there should be a way (button?) to easily report spammers or at least a given message as spam...

+1

AFAIK forum is being updated frequently, but it looks like it doesn't help